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Title: A genome-wide association study reveals genes associated with fusarium ear rot resistance in a maize core diversity panel

Author
item ZILA, CHARLES - North Carolina State University
item SAMAYOA, FERNANDO - Biological Mission Of Galicia Spain
item SANTIAGO, R - Biological Mission Of Galicia Spain
item BUTRON, A - Biological Mission Of Galicia Spain
item Holland, Jim - Jim

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/11/2013
Publication Date: 11/1/2013
Citation: Zila, C., Samayoa, F.L., Santiago, R., Butron, A., Holland, J.B. 2013. A genome-wide association study reveals genes associated with fusarium ear rot resistance in a maize core diversity panel. Genes, Genomes, Genetics. 3:2095-2104.

Interpretive Summary: Fusarium ear rot disease is common worldwide and can reduce yield. The causal fungus also can contaminate corn grain with a mycotoxin hazardous to human and animal health. The disease cannot be controlled with fungicide, so breeding for resistance is needed. Using extensive field phenotyping and genome-wide association analysis of a core diversity maize panel, we identified three SNPs associated with resistance. Two of the SNPs were inside or adjacent to genes with predicted functions that could be associated with disease resistance. Breeders could select for resistance alleles associated with these SNPs from unadapted maize for incorporation into elite breeding pools.

Technical Abstract: Fusarium ear rot is a common disease of maize that affects food and feed quality globally. Resistance to the disease is highly quantitative, and maize breeders have difficulty incorporating polygenic resistance alleles from unadapted donor sources into elite breeding populations without having a negative impact on agronomic performance. Identification of specific allele variants contributing to improved resistance may be useful to breeders by allowing selection of resistance alleles in coupling phase linkage with favorable agronomic characteristics. We report the results of a genome-wide association study (GWAS) to detect allele variants associated with increased resistance to Fusarium ear rot in a maize core diversity panel of 267 inbred lines evaluated in two sets of environments. We performed association tests with 47,445 SNPs while controlling for background genomic relationships with a mixed model and identified three marker loci significantly associated with disease resistance in at least one subset of environments. Each associated SNP locus had relatively small additive effects on disease resistance (±1.1% on a 0-100% scale), but nevertheless were associated with 3 to 12% of the genotypic variation within or across environment subsets. Two of three identified SNPs colocalized with genes that have been implicated with programmed cell death and were expressed at highest levels during the onset of disease symptoms. An analysis of associated allele frequencies within the major maize subpopulations revealed enrichment for resistance alleles in the tropical/subtropical and popcorn subpopulations compared to other temperate breeding pools.